You are missing a critical point... qx/COMMANDLINE/ or system("COMMANDLINE") invokes /bin/sh with the -c option like so: (on WIN32, this is of course a little different)

    execl("/bin/sh", "-c", COMMANDLINE);
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The quotes in COMMANDLINE are not being ignored or parsed by Perl. They are being handled by /bin/sh. Notice that at a /bin/sh prompt, if you were to type:

$ echo "Hello World"
Hello World
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For the original example, the poster was trying to do:

$ SQLCOMMAND; | sqlplus ...

It should have been:

$ echo "SQLCOMMAND;" | sqlplus ...

The shell uses the quotes to group arguments. The quotes are not passed through to the command (again, under WIN32, this is a little more convoluted).

The original problem posted was two-fold. First, as the initial responder suggested, the poster should have used 'echo "SQLCOMMAND;"' not 'SQLCOMMAND;'. As a later responder suggested, the poster should not be using both qx// and system() as both will execute the command. Either system() should be used if the output does not need to be intercepted, or qx// should be used if the output does need to be intercepted.